* using log directory 'd:/RCompile/CRANincoming/R-devel/gghic.Rcheck' * using R Under development (unstable) (2024-10-22 r87265 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'gghic/DESCRIPTION' ... OK * this is package 'gghic' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... WARNING Maintainer: 'Minghao Jiang ' New submission Possibly misspelled words in DESCRIPTION: GGHIC (2:8) Genomic (2:41) genomic (9:66) ggplot (3:9, 10:28) Strong dependencies not in mainstream repositories: biovizBase, Gviz, txdbmaker The Title field starts with the package name. Size of tarball: 47488777 bytes * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'gghic' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: 'LICENSE.md' 'data-raw' 'gghic.Rproj' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [19s] OK * checking whether the package can be loaded with stated dependencies ... [18s] OK * checking whether the package can be unloaded cleanly ... [18s] OK * checking whether the namespace can be loaded with stated dependencies ... [17s] NOTE Warning in dir.create(path) : cannot create dir 'C:\Users\CRAN\AppData\Local\gghic\gghic\Cache', reason 'No such file or directory' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... [18s] OK * checking loading without being on the library search path ... [19s] OK * checking whether startup messages can be suppressed ... [18s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [82s] NOTE add_columns: no visible binding for global variable 'cum_len' adjust_coordinates: no visible binding for global variable 'cum_len' adjust_coordinates: no visible binding for global variable 'orignal_start' adjust_coordinates2: no visible binding for global variable 'cum_len' adjust_coordinates2: no visible binding for global variable 'orignal_start' calculate_add_lengths: no visible binding for global variable 'seqnames1' calculate_add_lengths: no visible binding for global variable 'end1' calculate_add_lengths: no visible binding for global variable 'start1' calculate_add_lengths: no visible binding for global variable 'cum_len' calculate_hic_coordinates: no visible binding for global variable 'end1' calculate_hic_coordinates: no visible binding for global variable 'start2' calculate_hic_coordinates: no visible binding for global variable 'start1' calculate_hic_coordinates: no visible binding for global variable 'end2' calculate_hic_coordinates: no visible binding for global variable 'x' calculate_hic_coordinates: no visible binding for global variable 'xmin' calculate_hic_coordinates: no visible binding for global variable 'xmax' calculate_hic_coordinates: no visible binding for global variable 'xend' calculate_subtract_lengths: no visible binding for global variable 'seqnames1' calculate_subtract_lengths: no visible binding for global variable 'start1' extract_trs : : no visible global function definition for 'width' gghic: no visible binding for global variable 'score' gghic: no visible binding for global variable 'seqnames1' gghic: no visible binding for global variable 'start1' gghic: no visible binding for global variable 'end1' gghic: no visible binding for global variable 'seqnames2' gghic: no visible binding for global variable 'start2' gghic: no visible binding for global variable 'end2' retrive_cytoband: no visible binding for global variable 'chrom' retrive_cytoband: no visible binding for global variable 'c(cols, posCols)' retrive_cytoband: no visible binding for global variable 'chromStart' retrive_cytoband: no visible binding for global variable 'gieStain' retrive_cytoband: no visible binding for global variable 'chromEnd' retrive_genes: no visible binding for global variable 'gene_symbol' retrive_genes : : no visible binding for global variable 'gene_id' retrive_genes : : no visible binding for global variable 'gene_symbol' sub_columns: no visible binding for global variable 'orignal_start' Undefined global functions or variables: c(cols, posCols) chrom chromEnd chromStart cum_len end1 end2 gene_id gene_symbol gieStain orignal_start score seqnames1 seqnames2 start1 start2 width x xend xmax xmin * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [27s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... Check process probably crashed or hung up for 20 minutes ... killed Most likely this happened in the example checks (?), if not, ignore the following last lines of example output: > ##D ggplot2::ggplot( > ##D ggplot2::aes( > ##D seqnames1 = seqnames1, start1 = start1, end1 = end1, > ##D seqnames2 = seqnames2, start2 = start2, end2 = end2, > ##D fill = score > ##D ) > ##D ) + > ##D geom_hic() + > ##D theme_hic() > ## End(Not run) > > > > base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") > base::cat("theme_hic", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > ### *